One thing you can do is put some weight on the tray before re-applying silicone. This is especially true if the tray is GRP or similar as these tend to flex quite a bit. If its a resin tray then it's unlikely to flex much unless v poorly fitted. As has been mentioned, Dow 785 is a v. good choice and I've been using it for years and recommend it highly.
A couple of bags of sand in the tray (approximate the weight of a person) will cause the tray to deflect a little. Gun the silicone in and smooth off and once the silicone has set, remove the weight. Effectively the silicone will be compressed a little until someone stands in the tray when it will stretch to the neutral state in which it was applied.
When someone uses the tray the silicone should then be better able to cope with any movement.
HTH